26 papers · ranked by Valyu relevance
Anthony T. Bogetti, Jeremy M. G. Leung, Lillian T. Chong
The pathways by which a molecular process transitions to a target state are highly sought-after as direct views of a transition mechanism. While great strides have been made in the physics-based simulation of such pathways, the analysis of these pathways can be a major challenge due to their diversity and variable…
Iver Petersen, Katharina Kubatzky, Elisabeth Seebach
The focus of pathology as a biomedical discipline is the identification of the pathomechanisms of diseases and the integration of this knowledge into routine diagnosis and classification. Standard tools are macroscopic and microscopic analysis complemented by immunohistochemistry and molecular pathology. So far…
Gianluca Mattei, Daniel C. Zielinski, Zhuohui Gan, Matteo Ramazzotti + 1 more
Analyzing biological data using pathways helps identify trends in data tied to the function of a network. A large number of pathway-based analysis tools have been developed toward this goal. These pathways are often manually curated and thus associations are subject to the biases of the curator. A potentially…
Sriganesh Srihari, Mark A. Ragan
Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a key role in systems biology by complementing theoretical and experimental…
Melissa D. Walker, Gabrielle E. Giese, Amy D. Holdorf, Sushila Bhattacharya + 14 more
In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology and the response to therapeutic drugs. On March 15, 2020, a stay-at-home order was put into effect in the state of Massachusetts, USA, to flatten the curve of the spread of the…
P.J. Gawthrop, Edmund J. Crampin
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about steady-state mass flows (reaction rates) through the network. In this work we show how…
Martin Garrido-Rodriguez, Clement Potel, Mira Lea Burtscher, Isabelle Becher + 4 more
Cellular signaling plays a vital role in how cells communicate and adapt to both environmental and internal cues. At the molecular level, signaling is largely driven by phosphorylation cascades controlled by kinases. Because of this, kinase-driven signaling pathways are used as a conceptual framework to interpret…
Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett + 1 more
'Lydia E. Kavraki'] Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synthesizing these traditionally plant-derived compounds in genetically modified yeast cells…
Dhiman Ray, Michele Parrinello
Studying the pathways of ligand-receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein-ligand complexes can be computed using molecular dynamics (MD) simulations, often in quantitative agreement with experiments. However, only…
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen, Peter Dittrich + 1 more
'Daniel Merkle'] Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for pathways in reaction networks which is based on integer linear…
Yuan Luo, Chengsheng Mao
Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more…
Juyong Lee, In‐Ho Lee, InSuk Joung, Jooyong Lee + 1 more
We present a new computational approach to sample multiple reaction pathways with fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing method. This approach successfully samples not only the most dominant pathway but also many other possible…
Ryan Miller, Sebastian Muraru, Ana Belén Malpartida, Josh Low + 7 more
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while…
Wenbo Ma, Haifeng Zhang, Nianli Liu, Caiyue Li
Tumor molecular pathology has become an indispensable discipline for understanding cancer initiation, progression, therapeutic response, and clinical heterogeneity (1). By integrating histopathological assessment with genomic, transcriptomic, proteomic, immunological, and functional analyses, this field bridges…
Jana Weber, Pietro Lio’, Alexei Lapkin
Networks of chemical reactions represent relationships between molecules within chemical supply chains and promise to enhance planning of multi-step synthesis routes from bio-renewable feedstocks. This study aims to identify strategic molecules in chemical reaction networks that may potentially play a significant role…
Siddhartha Kundu
Biochemical networks integrate enzyme-mediated substrate conversions with non-enzymatic complex formation and disassembly to accomplish complex biochemical and physiological function. The multitude of theoretical studies utilizing empirical/clinical data notwithstanding, the parameters used in these analyses whilst…
Vidhi Kulkarni, Igor Tsigelny, Valentina Kouznetsova
Feline mammary carcinoma (FMC) is a prevalent and fatal carcinoma that predominantly affects unsprayed female cats. FMC is the third most common carcinoma in cats but is still underrepresented in research. Current diagnosis methods include physical examinations, imaging tests, and fine-needle aspiration. The diagnosis…
Stephen A. Bustin, Kurt A. Jellinger
The escalating impacts of the climate crisis, zoonotic spill-over, and antibiotic resistance have positioned molecular medicine at the forefront of pioneering translational research. With the rapid advances in modern medicine, the constantly evolving technologies of molecular pathology, diagnostics, and therapeutics…
Paul Wrede
Molecular biology is an established interdisciplinary field within biology that deals fundamentally with the function of any nucleic acid in the cellular context. The molecular biology section in Chemistry Central Journal focusses on the genetically determined chemistry and biochemistry occuring in the cell. How can…
Beatrice Collins, Jonathan Clayden, Jordan Berreur, Olivia Watts + 3 more
Living biological systems rely on the continuous operation of chemical reaction networks. These networks sustain out-of-equilibrium regimes in which chemical energy is continually converted into controlled mechanical work and motion. Out-of-equilibrium reaction networks have also enabled the design and successful…
Authors not listed
In 1985, during PhD research on catalytic cracking of cyclopentadiene dimers, we observed an unexpected phenomenon: certain hydrogen transfer reactions in bicyclic molecular systems exhibited dramatic yield differences depending on the reaction pathway. Two competing mechanisms were identified—a direct Diels-Alder…
Manish Kumar
Cancer is a complex disease having a number of composite problems to be considered including cancer immune evasion, therapy resistance, and recurrence for a cure. Fundamentally, it remains a genetic disease as diverse aspects of the complexity of tumor growth and cancer development relate to its genetic machinery and…
Alex Khodaverdian, Nir Yosef
The use of graphs as a way of abstracting and representing biological systems has provided a powerful analysis paradigm. Specifically, graph optimization algorithms are routinely used to address various connectivity queries, such as finding paths between proteins in a protein-protein interaction network, while…
K Stoeber
Molecular pathology, a rapidly expanding discipline connecting pathology and molecular biology, is providing a deeper insight and understanding of the molecular basis of the aetiology and pathogenesis of human disease. This well-laid-out book covers the basic principles of molecular pathology, explains the most…
Maria H. Rasmussen, Jan H. Jensen
We test our meta-molecular dynamics (MD) based approach for finding low-barrier (<30 kcal/mol) reactions (SciPost Chem. 2021, 1, 003) on uni- and bimolecular reactions extracted from the barrier dataset developed by Grambow et al. (Scientific Data 2020, 7, 137). For unimolecular reactions the meta-MD simulations…
Kazeem Olanrewaju, Ashlee N. Ford Versypt
The human physiological system consists of several biological units carefully organized to engage in a bio-physicochemical interaction with complex fluids transporting nutritional and life-supporting species (oxygen and carbon dioxide) needed for the proper functioning of the body. The nutritional species are products…